This line completes the alternating structure of the first four lines. If nature's first green, gold, doesn't stick around long, then it only makes sense that the first version of the leaf, which is the flower, doesn't stick around long either.
As the speaker says in this handy rhyme, the first leaf is a flower for only an hour. This doesn't literally mean that the trees or plants the speaker is referring to bloom for exactly an hour. But blooms, as you'll know if you've ever gardened, only last a few days, or weeks, depending on the plant.
Or, Frost could be talking about how, when the sun comes up, everything is golden and flower-like. But then, when the sun gets high in the sky and everything becomes its normal color, what once looked like golden flowers now look like what they truly are—green leaves.